Search found 6317 matches

by ted
Fri Jan 26, 2024 12:47 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 9825

Re: Somas not being positioned properly

I have to state that this mapping is as intended, and of little functional importance. Yes, it is of no functional imporance to the computer, but it will be a potential source of confusion to those who may read or reuse your code in the future. It's never a good idea to deliberately embed confusing...
by ted
Thu Jan 25, 2024 10:44 am
Forum: The GUI
Topic: Somas not being positioned properly
Replies: 7
Views: 9825

Re: Somas not being positioned properly

First, something unrelated: h.load_file('stdrun.hoc') h.load_file("stdlib.hoc") is unnecessary if you have already imported gui from neuron Now something related, although not necessarily the cause of the symptom you report: why iterate over x and y for row in range(x): for col in range(y)...
by ted
Wed Jan 24, 2024 11:35 am
Forum: Other questions
Topic: Out of range error (when applying high-voltage pulses)
Replies: 9
Views: 10501

Re: Out of range error (when applying high-voltage pulses)

I will need to be able to reproduce the problem. Please zip up the source code and email it to
ted dot carnevale at yale dot edu
and I will tell you what I find out.
by ted
Tue Jan 23, 2024 10:56 pm
Forum: Other questions
Topic: Out of range error (when applying high-voltage pulses)
Replies: 9
Views: 10501

Re: Out of range error (when applying high-voltage pulses)

As I recall, the original implementation by McIntyre & Grill didn't actually perturb extracellular potential. Instead, they used the "activating function" approach in which the effect of extracellular stimululation on the axon is represented by injecting a current into each compartment...
by ted
Mon Jan 22, 2024 1:56 pm
Forum: Other questions
Topic: Out of range error (when applying high-voltage pulses)
Replies: 9
Views: 10501

Re: Out of range error (when applying high-voltage pulses)

I hope you get an "out of range" error when the stimulus is 100 V. If you do this to living tissue, you'll fry something.
by ted
Mon Jan 22, 2024 1:54 pm
Forum: Other questions
Topic: Implementing extracellular stimulation
Replies: 14
Views: 73786

Re: Implementing extracellular stimulation

Bolus is a time honored term for qualitative description of the time course of injecting a drug, but not so for electrical stimulation, which has its own well established vocabulary. For the sake of clarity and mutual understanding, let's stick with the latter: one speaks of pulses or other waveform...
by ted
Sun Jan 21, 2024 3:18 pm
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

The ses file recreates the CellBuilder tool. The hoc file creates the model cell. If you have gone to the effort of using a CellBuilder to create a model specification, it's a good idea to save it to a ses file in case you want to change something later on (like disretization method, biophysical pro...
by ted
Thu Jan 18, 2024 11:01 am
Forum: Other questions
Topic: Implementing extracellular stimulation
Replies: 14
Views: 73786

Re: Implementing extracellular stimulation

What do you mean by "a singular point"?
What does "our wave form as a bolus" mean?
by ted
Wed Jan 17, 2024 12:53 am
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

Having read my previous post, someone might well ask "OK, Mr. Wizard, I have all the source code. How do I proceed?" First execute nrnivmodl to compile the mod files. Next create your own rig.ses file. 1. Execute nrngui 2. In the NEURON Main Menu toolbar click on Build/single compartment 3...
by ted
Tue Jan 16, 2024 11:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 20269

Re: Units in NMODL

Good questions. Also good to see that you're resolving documentation ambiguities by testing to see what syntax works and what doesn't. You might find it helpful to read chapter 9 of The NEURON Book. If you don't have the book, get this draft instead https://www.neuron.yale.edu/ftp/ted/book/revisions...
by ted
Tue Jan 16, 2024 3:15 pm
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

Here's the code that I used. The main file is called test.hoc. It starts with // model of monopolar extracellular stimulation of an axon // stimulus is a 100 us current pulse that drives extracellular potential load_file("nrngui.hoc") ///// create model cell load_file("axon.hoc")...
by ted
Mon Jan 15, 2024 10:52 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Units in NMODL
Replies: 6
Views: 20269

Re: Units in NMODL

I can't say I have ever seen a units declaration in the form sec_to_ms = (s) -> (ms) but then I haven't seen all NMODL code that has ever been written. Who knows, this might be the wave of the future. If a point process generates a current, that current must be in nanoamps. If a density (aka distrib...
by ted
Sun Jan 14, 2024 4:59 pm
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

Thank you. I'll review it and reply accordingly. In the meantime I decided to run a test of my own, using a simple model: cylindrical axon geometry: diam 1 um, length 1000 um, 0 end at 0,0,0, 1 end at 1000, 0, 0 (all units in um) biophysics: hh membrane at standard operating temperature (6.3 deg C),...
by ted
Fri Jan 12, 2024 3:17 pm
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

You could just zip up all the source files that are needed to reproduce your results (hoc, mod, ses, swc, txt, dat--but also see viewtopic.php?t=1048) and email them to ted dot carnevale at yale dot edu
by ted
Fri Jan 12, 2024 12:14 am
Forum: Getting started
Topic: d_lambda setup
Replies: 9
Views: 29730

Re: d_lambda setup

First, some important questions: What is your operational definition of "activating potential" (by what experimental procedure did you determine its numerical value)? Can you present a table of your results? An extracellular potential was applied to the axon. How? Specifically: What was yo...